rs12471074

Positions:

• chr2-161232463-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001199135.3(TANK):​c.1101+912C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 151,986 control chromosomes in the GnomAD database, including 1,650 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1650 hom., cov: 32)
• Consequence: TANK NM_001199135.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.433

Genes affected

TANK (HGNC:11562): (TRAF family member associated NFKB activator) The TRAF (tumor necrosis factor receptor-associated factor) family of proteins associate with and transduce signals from members of the tumor necrosis factor receptor superfamily. The protein encoded by this gene is found in the cytoplasm and can bind to TRAF1, TRAF2, or TRAF3, thereby inhibiting TRAF function by sequestering the TRAFs in a latent state in the cytoplasm. For example, the protein encoded by this gene can block TRAF2 binding to LMP1, the Epstein-Barr virus transforming protein, and inhibit LMP1-mediated NF-kappa-B activation. Three alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2010]

PSMD14-DT (HGNC:56104): (PSMD14 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.252 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TANK	NM_001199135.3	c.1101+912C>T		intron_variant		ENST00000392749.7	NP_001186064.1
PSMD14-DT	NR_110593.1	n.349-8980G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TANK	ENST00000392749.7	c.1101+912C>T		intron_variant		1	NM_001199135.3	ENSP00000376505	P1

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16697 AN: 151866 Hom.: 1633 Cov.: 32

Gnomad AFR AF: 0.256

Gnomad AMI AF: 0.00329

Gnomad AMR AF: 0.0679

Gnomad ASJ AF: 0.0582

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.0842

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0364

Gnomad OTH AF: 0.0911

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.110 AC: 16765 AN: 151986 Hom.: 1650 Cov.: 32 AF XY: 0.111 AC XY: 8277 AN XY: 74304

Gnomad4 AFR AF: 0.256

Gnomad4 AMR AF: 0.0678

Gnomad4 ASJ AF: 0.0582

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.0845

Gnomad4 FIN AF: 0.0842

Gnomad4 NFE AF: 0.0364

Gnomad4 OTH AF: 0.0963

Alfa AF: 0.0764 Hom.: 129

Bravo AF: 0.115

Asia WGS AF: 0.185 AC: 640 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	14
DANN	Benign	0.59

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs12471074; hg19: chr2-162088974;